Avoiding Incomplete Upgrade of SAP Host Agent 
We recommend that you create an empty file called .upgrading in the $DIR_NEW directory to avoid that saphostexec starts the upgrade procedure during the extraction of SAPHOSTAGENT.SAR – with the consequence that only part of the newest version of the packages is upgraded.
Create the .upgrading file in the $DIR_NEW directory.
Extract SAPHOSTAGENT.SAR to $DIR_NEW.
Remove .upgrading from the $DIR_NEW directory.
> cd /usr/sap/hostctrl/new/
> touch .upgrading
> SAPCAR -xvf SAPHOSTAGENT.SAR
> rm .upgrading